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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:MCL1-CLNS1A (FusionGDB2 ID:52200)

Fusion Gene Summary for MCL1-CLNS1A

check button Fusion gene summary
Fusion gene informationFusion gene name: MCL1-CLNS1A
Fusion gene ID: 52200
HgeneTgene
Gene symbol

MCL1

CLNS1A

Gene ID

4170

1207

Gene nameMCL1 apoptosis regulator, BCL2 family memberchloride nucleotide-sensitive channel 1A
SynonymsBCL2L3|EAT|MCL1-ES|MCL1L|MCL1S|Mcl-1|TM|bcl2-L-3|mcl1/EATCLCI|CLNS1B|ICln
Cytomap

1q21.2

11q14.1

Type of geneprotein-codingprotein-coding
Descriptioninduced myeloid leukemia cell differentiation protein Mcl-1BCL2 family apoptosis regulatorMCL1, BCL2 family apoptosis regulatorbcl-2-like protein 3bcl-2-related protein EAT/mcl1myeloid cell leukemia 1myeloid cell leukemia ESmyeloid cell leukemia semethylosome subunit pIClnchloride channel regulatory proteinchloride channel, nucleotide sensitive 1Achloride conductance regulatory protein IClnchloride ion current inducer proteini(Cln)reticulocyte pIClnreticulocyte protein ICln
Modification date2020032220200313
UniProtAcc

Q07820

P54105

Ensembl transtripts involved in fusion geneENST00000369026, ENST00000307940, 
ENST00000464132, 		ENST00000263309, 
ENST00000525064, ENST00000525428, 
ENST00000528364, ENST00000532069, 
ENST00000533957, 
Fusion gene scores* DoF score12 X 12 X 5=72010 X 8 X 6=480
# samples 1413
** MAII scorelog2(14/720*10)=-2.36257007938471
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(13/480*10)=-1.88452278258006
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MCL1 [Title/Abstract] AND CLNS1A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMCL1(150547030)-CLNS1A(77298741), # samples:1
Anticipated loss of major functional domain due to fusion event.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneMCL1

GO:0034097

response to cytokine

9184696

HgeneMCL1

GO:0043066

negative regulation of apoptotic process

20041405

TgeneCLNS1A

GO:0000387

spliceosomal snRNP assembly

18984161


check buttonFusion gene breakpoints across MCL1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across CLNS1A (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChiTaRS5.0N/AAV685436MCL1chr1

150547030

-CLNS1Achr11

77298741

+


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Fusion Gene ORF analysis for MCL1-CLNS1A

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
5CDS-intronENST00000369026ENST00000263309MCL1chr1

150547030

-CLNS1Achr11

77298741

+
5CDS-intronENST00000369026ENST00000525064MCL1chr1

150547030

-CLNS1Achr11

77298741

+
5CDS-intronENST00000369026ENST00000525428MCL1chr1

150547030

-CLNS1Achr11

77298741

+
5CDS-intronENST00000369026ENST00000528364MCL1chr1

150547030

-CLNS1Achr11

77298741

+
5CDS-intronENST00000369026ENST00000532069MCL1chr1

150547030

-CLNS1Achr11

77298741

+
5CDS-intronENST00000369026ENST00000533957MCL1chr1

150547030

-CLNS1Achr11

77298741

+
intron-intronENST00000307940ENST00000263309MCL1chr1

150547030

-CLNS1Achr11

77298741

+
intron-intronENST00000307940ENST00000525064MCL1chr1

150547030

-CLNS1Achr11

77298741

+
intron-intronENST00000307940ENST00000525428MCL1chr1

150547030

-CLNS1Achr11

77298741

+
intron-intronENST00000307940ENST00000528364MCL1chr1

150547030

-CLNS1Achr11

77298741

+
intron-intronENST00000307940ENST00000532069MCL1chr1

150547030

-CLNS1Achr11

77298741

+
intron-intronENST00000307940ENST00000533957MCL1chr1

150547030

-CLNS1Achr11

77298741

+
intron-intronENST00000464132ENST00000263309MCL1chr1

150547030

-CLNS1Achr11

77298741

+
intron-intronENST00000464132ENST00000525064MCL1chr1

150547030

-CLNS1Achr11

77298741

+
intron-intronENST00000464132ENST00000525428MCL1chr1

150547030

-CLNS1Achr11

77298741

+
intron-intronENST00000464132ENST00000528364MCL1chr1

150547030

-CLNS1Achr11

77298741

+
intron-intronENST00000464132ENST00000532069MCL1chr1

150547030

-CLNS1Achr11

77298741

+
intron-intronENST00000464132ENST00000533957MCL1chr1

150547030

-CLNS1Achr11

77298741

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for MCL1-CLNS1A


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for MCL1-CLNS1A


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:150547030/:77298741)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
MCL1

Q07820

CLNS1A

P54105

FUNCTION: Involved in the regulation of apoptosis versus cell survival, and in the maintenance of viability but not of proliferation. Mediates its effects by interactions with a number of other regulators of apoptosis. Isoform 1 inhibits apoptosis. Isoform 2 promotes apoptosis. {ECO:0000269|PubMed:10766760, ECO:0000269|PubMed:16543145}.FUNCTION: Involved in both the assembly of spliceosomal snRNPs and the methylation of Sm proteins (PubMed:21081503, PubMed:18984161). Chaperone that regulates the assembly of spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. In the cytosol, the Sm proteins SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG are trapped in an inactive 6S pICln-Sm complex by the chaperone CLNS1A that controls the assembly of the core snRNP. Dissociation by the SMN complex of CLNS1A from the trapped Sm proteins and their transfer to an SMN-Sm complex triggers the assembly of core snRNPs and their transport to the nucleus. May also indirectly participate in cellular volume control by activation of a swelling-induced chloride conductance pathway. {ECO:0000269|PubMed:10330151, ECO:0000269|PubMed:11713266, ECO:0000269|PubMed:18984161, ECO:0000269|PubMed:21081503}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page


* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for MCL1-CLNS1A


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for MCL1-CLNS1A


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for MCL1-CLNS1A


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for MCL1-CLNS1A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource